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PLoS One. 2015 Aug 4;10(8):e0131217. doi: 10.1371/journal.pone.0131217. eCollection 2015.

Selection of Orthologous Genes for Construction of a Highly Resolved Phylogenetic Tree and Clarification of the Phylogeny of Trichosporonales Species.

Author information

1
Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
2
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumiku, Yokohama, Kanagawa, 230-0045, Japan.
3
Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Yayoi, Bunkyoku, Tokyo, 113-0032, Japan.
4
Planning, in silico biology, inc., SOHO Station 706, 24-8 Yamashita-cho, Naka-ku, Yokohama, Kanagawa, 231-0023 Japan.
5
Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo, 204-8588, Japan.

Abstract

The order Trichosporonales (Tremellomycotina, Basidiomycota) includes various species that have clinical, agricultural and biotechnological value. Thus, understanding why and how evolutionary diversification occurred within this order is extremely important. This study clarified the phylogenetic relationships among Tricosporonales species. To select genes suitable for phylogenetic analysis, we determined the draft genomes of 17 Trichosporonales species and extracted 30 protein-coding DNA sequences (CDSs) from genomic data. The CDS regions of Trichosporon asahii and T. faecale were identified by referring to mRNA sequence data since the intron positions of the respective genes differed from those of Cryptococcus neoformans (outgroup) and are not conserved within this order. A multiple alignment of the respective gene was first constructed using the CDSs of T. asahii, T. faecale and C. neoformans, and those of other species were added and aligned based on codons. The phylogenetic trees were constructed based on each gene and a concatenated alignment. Resolution of the maximum-likelihood trees estimated from the concatenated dataset based on both nucleotide (72,531) and amino acid (24,173) sequences were greater than in previous reports. In addition, we found that several genes, such as phosphatidylinositol 3-kinase TOR1 and glutamate synthase (NADH), had good resolution in this group (even when used alone). Our study proposes a set of genes suitable for constructing a phylogenetic tree with high resolution to examine evolutionary diversification in Trichosporonales. These can also be used for epidemiological and biogeographical studies, and may also serve as the basis for a comprehensive reclassification of pleomorphic fungi.

PMID:
26241762
PMCID:
PMC4524599
DOI:
10.1371/journal.pone.0131217
[Indexed for MEDLINE]
Free PMC Article

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